Inhalt

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   Title
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   Summary
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   Zusammenfassung
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   Table of Contents
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   List of Publications
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   List of Conference Proceedings
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   List of Posters
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   List of Patents
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   List of Abbreviations
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   List of Symbols
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   List of Figures
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   List of Tables
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   1 Industrial biotechnology
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   2 Population heterogeneity
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   3 Single cell analysis
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  4 Microfluidics
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  4.1 Theory
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   4.1.1 Convective mass transport
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   4.1.2 Diffusive mass transport
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   4.2 Fabrication of microfluidic devices
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   5 Microfluidic single cell analysis
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   5.1 Single cell trapping in microfluidics
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   5.1.1 Non-surface contact single-cell trapping
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   5.1.2 Surface contact single cell trapping mechanisms
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   Publications
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   6 Publication I - Polydimethylsiloxane (PDMS) Sub-Micron Traps for Single-Cell Analysis of Bacteria
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   6.1 Abstract
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   6.2 Introduction
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  6.3 Experimental
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   6.3.1 Soft Lithography
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   6.3.2 Sample Preparation
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   6.3.3 Experimental Procedure
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  6.4 Results and Discussion
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   6.4.1 Trap Layout and Geometry
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   6.4.2 Numerical Simulation
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   6.4.3 Single Cell Cultivation
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   6.5 Conclusions
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   7 Publication II - Spatiotemporal microbial single-cell analysis using a high-throughput microfluidics cultivation platform
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   7.1 Abstract
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   7.2 Introduction
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  7.3 Materials and Methods
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   7.3.1 Device fabrication and setup
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   7.3.2 Flow characterization
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   7.3.3 Bacterial strains and pre-cultivation
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   7.3.4 Microfluidic cultivation
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   7.3.5 Time-lapse imaging
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   7.3.6 Image analysis and data visualization
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   7.3.7 Flow cytometry (FC)
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   7.3.8 Computational fluid dynamics
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  7.4 Results
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   7.4.1 Device layout and principle
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   7.4.2 Flow tracer analysis
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   7.4.3 Computational fluid dynamics
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   7.4.4 Microbial single-cell analysis of isogenic microcolonies
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   7.4.5 Identifying rare cellular events in C. glutamicum
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   7.4.6 Dynamics of spontaneously induced SOS in single C. glutamicum cells
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   7.4.7 High-throughput screening of SOS+ cells
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   7.5 Discussion
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   7.6 Conclusions
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  7.7 Publication II Supplement
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   7.7.1 Publication II - Supplement 1
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  7.7.2 Publication II - Supplement 2
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   7.7.2.1 Frequency of spontaneously SOS+ induced cells at MGC at various gatings
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   7.7.2.2 Occurrence of spontaneously induced cells
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  7.7.3 Publication II - Supplement 3
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   7.7.3.1 Occurrence of spontaneously induced cells vs. total number of analyzed cells
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   7.7.3.2 Determination of SOS positive cells for FC measurements
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   8 Publication III - Rapid inoculation of single bacteria into parallel picoliter fermentation chambers
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   8.1 Abstract
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   8.2 Introduction
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  8.3 Materials and Methods
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   8.3.1 Chip fabrication
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   8.3.2 Device configuration
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   8.3.3 Experimental setup
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   8.3.4 Bubble injection and cell inoculation procedure
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   8.3.5 Fluorescent flow tracer analysis
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   8.3.6 Cultivation of C. glutamicum
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  8.4 Results and discussion
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   8.4.1 Single-cell inoculation procedure
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   8.4.2 Flow tracer characterization
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   8.4.3 Air bubble injection
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   8.4.4 Air bubble diffusion
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   8.4.5 Cell loading performance
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   8.4.6 Viability and cell growth
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   8.5 Conclusion
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  8.6 Publication III Supplement
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   8.6.1 Publication III - Capillary force calculation
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   8.6.2 Publication III - Fitting of experimental data
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   9 Publication IV - Microfluidic growth chambers with optical tweezers for full spatial single-cell control and analysis of evolving microbes
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   9.1 Abstract
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   9.2 Introduction
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  9.3 Materials and Methods
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   9.3.1 Fabrication of microfluidic growth chambers
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   9.3.2 Experimental microscopy setup
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   9.3.3 Cultivation of Escherichia coli
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   9.3.4 Cultivation in microfluidic chambers
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   9.3.5 Image analysis and data evaluation
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   9.3.6 Device principle and design
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  9.4 Results and Discussion
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   9.4.1 Growth in microenvironments
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   9.4.2 OT control over single cells
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   9.5 Conclusion and outlook
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   10 Future Perspectives
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   10.1 Batch cultivation in microfluidic devices
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   10.2 Flow control of liquids in microfluidic devices
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  10.2.1 Fabrication procedure of membrane pumps
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   10.2.1.1 Fabrication of microfluidic master molds
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   10.2.1.2 PDMS multilayer chip fabrication
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   10.2.2 Device design and principle
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   10.2.3 Experimental setup
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   10.2.4 Particle image velocimetry
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   10.2.5 Characterization of flow rates
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   10.2.6 Pulsation in flow
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   10.2.7 Conclusion and outlook
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   10.3 Control of oxygen levels in microfluidic devices
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   11 References
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  12 Supplemental information
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  12.1 Fabrication of multilayered microfluidic devices
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   12.1.1 Master mold fabrication
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   12.1.2 PDMS replica molding
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  12.2 Determination of pulsation rate
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   12.2.1 Rectangular shaped cross-section
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   12.2.2 Ellipsoid shaped cross-section
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   12.2.3 Coefficient of determination
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   12.3 Changing oxygen concentrations vs. flow rate